getAnnotation: Download exon information for a given genome

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

Description

Using the GenomicFeatures package and the UCSC genome browser, creates a data frame of exons (one exon per row) for the specified genome.

Usage

getAnnotation(genome, tablename, genes = TRUE, verbose = TRUE)

Arguments

genome	Genome (species) for which annotation is desired. A list of supported genomes can be found using rtracklayer:::ucscGenomes()[,"db"]; details on each genome can be seen using rtracklayer:::ucscGenomes().
tablename	UCSC table from which to download exon information. Use supportedTables(genome) to get a list of supported tables for genome.
genes	If TRUE (as it is by default), each exon in the resulting data frame is labeled with the gene it belongs to. Gene information is not available in every table. If FALSE, each exon in the resulting data frame is labeled with the transcript it belongs to.
verbose	If TRUE, updates are printed on screen as annotation download progresses.

Value

A data frame (one row per exon) giving the exon's gene or transcript, location (start/end), and possibly other information.

Note

This function interacts with the online UCSC Genome Browser, so internet connection is required to use this function, and connection speed affects function speed.

Author(s)

Alyssa Frazee

Examples

## Not run: 
mouse.exons <- getAnnotation("mm9","refGene")
head(mouse.exons)

## End(Not run)

leekgroup/derfinder documentation built on May 20, 2019, 11:30 p.m.